Comments (5)
moold
commented on May 26, 2024
Could you try again and check this bug is still existed ?
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ShuChen1986
commented on May 26, 2024
Could you try again and check this bug is still existed ?
I have tried several times, with different parallel jobs and threads, all got back with the same issue.
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moold
commented on May 26, 2024
Could you paste the content of log file: 05.polish.ref.sh.e to here?
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ShuChen1986
commented on May 26, 2024
As I have said, there is no error reported, but the job just was not running. No CPU was observed runing the script.
hostname
+ hostname
cd /home/user/necat/stylo/Nextpolish-ex/01_rundir/01.kmer_count/05.polish.ref.sh.work/polish_genome0
+ cd /home/user/necat/stylo/Nextpolish-ex/01_rundir/01.kmer_count/05.polish.ref.sh.work/polish_genome0
time python /home/user/Music/NextPolish/lib/nextPolish.py -p 2 -g /home/user/necat/stylo/Nextpolish-ex/./01_rundir/01.kmer_count/input.genome.fasta -b /home/user/necat/stylo/Nextpolish-ex/./01_rundir/01.kmer_count/input.genome.fasta.blc -i 0 -t 2 -s /home/user/necat/stylo/Nextpolish-ex/./01_rundir/01.kmer_count/sgs.sort.bam -l /home/user/necat/stylo/Nextpolish-ex/./01_rundir/01.kmer_count/lgs.sort.bam -o genome.nextpolish.part000.fasta
+ time python /home/user/Music/NextPolish/lib/nextPolish.py -p 2 -g /home/user/necat/stylo/Nextpolish-ex/./01_rundir/01.kmer_count/input.genome.fasta -b /home/user/necat/stylo/Nextpolish-ex/./01_rundir/01.kmer_count/input.genome.fasta.blc -i 0 -t 2 -s /home/user/necat/stylo/Nextpolish-ex/./01_rundir/01.kmer_count/sgs.sort.bam -l /home/user/necat/stylo/Nextpolish-ex/./01_rundir/01.kmer_count/lgs.sort.bam -o genome.nextpolish.part000.fasta
[INFO] 2019-11-18 19:35:11,879 Polished step options:
[INFO] 2019-11-18 19:35:11,879 Namespace(bam_lgs='/home/user/necat/stylo/Nextpolish-ex/./01_rundir/01.kmer_count/lgs.sort.bam', bam_sgs='/home/user/necat/stylo/Nextpolish-ex/./01_rundir/01.kmer_count/sgs.sort.bam', block='/home/user/necat/stylo/Nextpolish-ex/./01_rundir/01.kmer_count/input.genome.fasta.blc', block_index='0', count_read_ins_sgs=10000, debug=False, ext_len_edge=2, genome='/home/user/necat/stylo/Nextpolish-ex/./01_rundir/01.kmer_count/input.genome.fasta', indel_balance_factor_lgs=0.33, indel_balance_factor_sgs=0.5, max_clip_ratio_lgs=0.4, max_clip_ratio_sgs=0.15, max_count_kmer=50, max_indel_factor_lgs=0.21, max_ins_fold_sgs=5, max_ins_len_sgs=10000, max_len_kmer=50, max_snp_factor_lgs=0.53, max_variant_count_lgs=150000, min_count_ratio_skip=0.8, min_count_snp=5, min_count_snp_link=5, min_depth_snp=3, min_len_inter_kmer=5, min_len_ldr=3, min_map_quality=0, min_snp_factor_sgs=0.34, out='genome.nextpolish.part000.fasta', ploidy=2, process=2, task=2, trim_len_edge=2)
[INFO] 2019-11-18 19:35:12,175 Start a polished worker in 27266 from parent 27264
[INFO] 2019-11-18 19:35:12,174 Start a polished worker in 27265 from parent 27264
[INFO] 2019-11-18 20:08:58,770 Start a polished worker in 27665 from parent 27264
[INFO] 2019-11-18 20:16:46,497 Start a polished worker in 27669 from parent 27264
[INFO] 2019-11-18 20:43:39,934 Start a polished worker in 27682 from parent 27264
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moold
commented on May 26, 2024
It seems two threads crashed. I need to reproduce this error to debug what was happened. I am not sure whether you can send me the input data: contig sequences and its corresponding bam files? you can extract only one contig sequence which can induce this error and its corresponding bam file.
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